Starting phenix.real_space_refine on Fri Feb 16 21:14:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2j_32262/02_2024/7w2j_32262_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2j_32262/02_2024/7w2j_32262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2j_32262/02_2024/7w2j_32262.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2j_32262/02_2024/7w2j_32262.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2j_32262/02_2024/7w2j_32262_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w2j_32262/02_2024/7w2j_32262_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 12 7.16 5 P 4 5.49 5 S 90 5.16 5 C 10438 2.51 5 N 2856 2.21 5 O 3122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 92": "OD1" <-> "OD2" Residue "A PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A ASP 491": "OD1" <-> "OD2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 97": "OE1" <-> "OE2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 129": "OE1" <-> "OE2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 433": "OD1" <-> "OD2" Residue "D ASP 92": "OD1" <-> "OD2" Residue "D PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 468": "OE1" <-> "OE2" Residue "D ASP 491": "OD1" <-> "OD2" Residue "E PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 136": "OE1" <-> "OE2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "E TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 97": "OE1" <-> "OE2" Residue "F TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 129": "OE1" <-> "OE2" Residue "F PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 186": "OD1" <-> "OD2" Residue "F PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 433": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16522 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4143 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 36, 'TRANS': 500} Chain: "B" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 4 Chain: "C" Number of atoms: 3149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3149 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 25, 'TRANS': 392} Chain breaks: 1 Chain: "D" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4143 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 36, 'TRANS': 500} Chain: "E" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 4 Chain: "F" Number of atoms: 3149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3149 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 25, 'TRANS': 392} Chain breaks: 1 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'HEC': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'HEC': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1743 SG CYS A 226 52.601 34.063 74.352 1.00 8.79 S ATOM 1714 SG CYS A 222 51.682 31.454 77.344 1.00 8.19 S ATOM 1674 SG CYS A 216 53.050 28.269 73.790 1.00 25.28 S ATOM 9815 SG CYS D 226 49.606 92.808 74.348 1.00 8.27 S ATOM 9786 SG CYS D 222 50.524 95.415 77.342 1.00 9.35 S ATOM 9746 SG CYS D 216 49.156 98.602 73.790 1.00 12.48 S Time building chain proxies: 9.46, per 1000 atoms: 0.57 Number of scatterers: 16522 At special positions: 0 Unit cell: (103.077, 127.745, 119.816, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 12 26.01 S 90 16.00 P 4 15.00 O 3122 8.00 N 2856 7.00 C 10438 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=32, symmetry=0 Number of additional bonds: simple=32, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.52 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A 602 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 226 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " pdb="FE4 F3S A 602 " - pdb=" SG CYS A 216 " pdb=" F3S D 602 " pdb="FE1 F3S D 602 " - pdb=" SG CYS D 226 " pdb="FE3 F3S D 602 " - pdb=" SG CYS D 222 " pdb="FE4 F3S D 602 " - pdb=" SG CYS D 216 " Number of angles added : 18 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3860 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 12 sheets defined 32.3% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.76 Creating SS restraints... Processing helix chain 'A' and resid 17 through 29 Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 93 through 96 Processing helix chain 'A' and resid 106 through 109 Processing helix chain 'A' and resid 122 through 129 removed outlier: 4.010A pdb=" N LEU A 125 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N HIS A 126 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR A 129 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 356 through 359 removed outlier: 4.236A pdb=" N SER A 359 " --> pdb=" O ASP A 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 356 through 359' Processing helix chain 'A' and resid 374 through 383 Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 441 through 461 Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 523 through 541 removed outlier: 4.269A pdb=" N ARG A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASP A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 55 No H-bonds generated for 'chain 'B' and resid 52 through 55' Processing helix chain 'B' and resid 75 through 82 removed outlier: 3.754A pdb=" N ALA B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 92 removed outlier: 4.248A pdb=" N LYS B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA B 92 " --> pdb=" O THR B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 126 through 129 No H-bonds generated for 'chain 'B' and resid 126 through 129' Processing helix chain 'C' and resid 42 through 50 removed outlier: 3.544A pdb=" N ALA C 47 " --> pdb=" O GLY C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 105 removed outlier: 3.530A pdb=" N ALA C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 123 No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 128 through 140 removed outlier: 3.508A pdb=" N LYS C 132 " --> pdb=" O ASP C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 171 removed outlier: 3.532A pdb=" N GLY C 165 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS C 168 " --> pdb=" O GLY C 165 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 169 " --> pdb=" O ILE C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 195 removed outlier: 3.546A pdb=" N GLY C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 205 No H-bonds generated for 'chain 'C' and resid 202 through 205' Processing helix chain 'C' and resid 246 through 255 removed outlier: 3.504A pdb=" N THR C 255 " --> pdb=" O GLN C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 280 through 291 removed outlier: 3.525A pdb=" N ALA C 285 " --> pdb=" O ALA C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 340 No H-bonds generated for 'chain 'C' and resid 337 through 340' Processing helix chain 'C' and resid 374 through 382 Processing helix chain 'C' and resid 409 through 422 removed outlier: 4.190A pdb=" N ALA C 413 " --> pdb=" O ASP C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 440 removed outlier: 3.872A pdb=" N VAL C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 453 through 470 removed outlier: 3.706A pdb=" N LEU C 459 " --> pdb=" O VAL C 455 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE C 468 " --> pdb=" O ILE C 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 44 through 53 Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 93 through 96 Processing helix chain 'D' and resid 106 through 109 Processing helix chain 'D' and resid 122 through 129 removed outlier: 4.010A pdb=" N LEU D 125 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N HIS D 126 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR D 129 " --> pdb=" O HIS D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 153 Proline residue: D 144 - end of helix Processing helix chain 'D' and resid 182 through 194 Processing helix chain 'D' and resid 234 through 244 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 356 through 359 removed outlier: 4.236A pdb=" N SER D 359 " --> pdb=" O ASP D 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 356 through 359' Processing helix chain 'D' and resid 374 through 383 Processing helix chain 'D' and resid 389 through 400 Processing helix chain 'D' and resid 441 through 461 Processing helix chain 'D' and resid 489 through 491 No H-bonds generated for 'chain 'D' and resid 489 through 491' Processing helix chain 'D' and resid 511 through 513 No H-bonds generated for 'chain 'D' and resid 511 through 513' Processing helix chain 'D' and resid 523 through 541 removed outlier: 4.270A pdb=" N ARG D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASP D 535 " --> pdb=" O LEU D 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 55 No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 75 through 82 removed outlier: 3.754A pdb=" N ALA E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 92 removed outlier: 4.249A pdb=" N LYS E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA E 92 " --> pdb=" O THR E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 124 No H-bonds generated for 'chain 'E' and resid 122 through 124' Processing helix chain 'E' and resid 126 through 129 No H-bonds generated for 'chain 'E' and resid 126 through 129' Processing helix chain 'F' and resid 42 through 50 removed outlier: 3.545A pdb=" N ALA F 47 " --> pdb=" O GLY F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 105 removed outlier: 3.530A pdb=" N ALA F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 123 No H-bonds generated for 'chain 'F' and resid 120 through 123' Processing helix chain 'F' and resid 128 through 140 removed outlier: 3.508A pdb=" N LYS F 132 " --> pdb=" O ASP F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 171 removed outlier: 3.532A pdb=" N GLY F 165 " --> pdb=" O ALA F 162 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS F 168 " --> pdb=" O GLY F 165 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE F 169 " --> pdb=" O ILE F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 195 removed outlier: 3.545A pdb=" N GLY F 191 " --> pdb=" O ASP F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 205 No H-bonds generated for 'chain 'F' and resid 202 through 205' Processing helix chain 'F' and resid 246 through 255 removed outlier: 3.504A pdb=" N THR F 255 " --> pdb=" O GLN F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 271 Processing helix chain 'F' and resid 275 through 277 No H-bonds generated for 'chain 'F' and resid 275 through 277' Processing helix chain 'F' and resid 280 through 291 removed outlier: 3.525A pdb=" N ALA F 285 " --> pdb=" O ALA F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 340 No H-bonds generated for 'chain 'F' and resid 337 through 340' Processing helix chain 'F' and resid 374 through 382 Processing helix chain 'F' and resid 409 through 422 removed outlier: 4.188A pdb=" N ALA F 413 " --> pdb=" O ASP F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 440 removed outlier: 3.871A pdb=" N VAL F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 450 No H-bonds generated for 'chain 'F' and resid 448 through 450' Processing helix chain 'F' and resid 453 through 470 removed outlier: 3.705A pdb=" N LEU F 459 " --> pdb=" O VAL F 455 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA F 467 " --> pdb=" O GLY F 463 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE F 468 " --> pdb=" O ILE F 464 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 284 through 287 removed outlier: 6.752A pdb=" N LYS A 247 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ASP A 37 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 249 " --> pdb=" O ASP A 37 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 87 through 89 Processing sheet with id= C, first strand: chain 'A' and resid 277 through 280 removed outlier: 6.182A pdb=" N TYR A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N VAL A 254 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 327 through 332 removed outlier: 3.690A pdb=" N ILE A 405 " --> pdb=" O MET A 329 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 331 " --> pdb=" O VAL A 403 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 70 through 72 Processing sheet with id= F, first strand: chain 'C' and resid 385 through 388 removed outlier: 3.735A pdb=" N THR C 388 " --> pdb=" O HIS C 391 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS C 391 " --> pdb=" O THR C 388 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 284 through 287 removed outlier: 6.751A pdb=" N LYS D 247 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ASP D 37 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE D 249 " --> pdb=" O ASP D 37 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 87 through 89 Processing sheet with id= I, first strand: chain 'D' and resid 277 through 280 removed outlier: 6.182A pdb=" N TYR D 271 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL D 254 " --> pdb=" O TYR D 271 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 327 through 332 removed outlier: 3.691A pdb=" N ILE D 405 " --> pdb=" O MET D 329 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE D 331 " --> pdb=" O VAL D 403 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 70 through 72 Processing sheet with id= L, first strand: chain 'F' and resid 385 through 388 removed outlier: 3.734A pdb=" N THR F 388 " --> pdb=" O HIS F 391 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS F 391 " --> pdb=" O THR F 388 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.77 Time building geometry restraints manager: 8.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.77: 16809 1.77 - 2.33: 157 2.33 - 2.89: 0 2.89 - 3.45: 0 3.45 - 4.01: 6 Bond restraints: 16972 Sorted by residual: bond pdb=" S4 F3S D 602 " pdb="FE1 F3S D 602 " ideal model delta sigma weight residual 2.233 4.007 -1.774 2.00e-02 2.50e+03 7.87e+03 bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 4.007 -1.774 2.00e-02 2.50e+03 7.86e+03 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 3.759 -1.501 2.00e-02 2.50e+03 5.63e+03 bond pdb=" S1 F3S D 602 " pdb="FE4 F3S D 602 " ideal model delta sigma weight residual 2.258 3.758 -1.500 2.00e-02 2.50e+03 5.63e+03 bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 3.463 -1.163 2.00e-02 2.50e+03 3.38e+03 ... (remaining 16967 not shown) Histogram of bond angle deviations from ideal: 36.03 - 64.50: 14 64.50 - 92.96: 30 92.96 - 121.43: 18833 121.43 - 149.89: 4313 149.89 - 178.35: 12 Bond angle restraints: 23202 Sorted by residual: angle pdb=" S3 F3S D 602 " pdb="FE1 F3S D 602 " pdb=" S4 F3S D 602 " ideal model delta sigma weight residual 112.59 60.22 52.37 3.00e+00 1.11e-01 3.05e+02 angle pdb=" S3 F3S A 602 " pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 112.59 60.24 52.35 3.00e+00 1.11e-01 3.05e+02 angle pdb=" S1 F3S D 602 " pdb="FE4 F3S D 602 " pdb=" S3 F3S D 602 " ideal model delta sigma weight residual 114.75 66.85 47.90 3.00e+00 1.11e-01 2.55e+02 angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S3 F3S A 602 " ideal model delta sigma weight residual 114.75 66.85 47.90 3.00e+00 1.11e-01 2.55e+02 angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S2 F3S A 602 " ideal model delta sigma weight residual 103.63 61.46 42.17 3.00e+00 1.11e-01 1.98e+02 ... (remaining 23197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.58: 9424 26.58 - 53.16: 494 53.16 - 79.74: 42 79.74 - 106.31: 20 106.31 - 132.89: 2 Dihedral angle restraints: 9982 sinusoidal: 3928 harmonic: 6054 Sorted by residual: dihedral pdb=" CA PHE A 80 " pdb=" C PHE A 80 " pdb=" N PRO A 81 " pdb=" CA PRO A 81 " ideal model delta harmonic sigma weight residual -180.00 -132.52 -47.48 0 5.00e+00 4.00e-02 9.02e+01 dihedral pdb=" CA PHE D 80 " pdb=" C PHE D 80 " pdb=" N PRO D 81 " pdb=" CA PRO D 81 " ideal model delta harmonic sigma weight residual -180.00 -132.58 -47.42 0 5.00e+00 4.00e-02 8.99e+01 dihedral pdb=" CA PHE F 156 " pdb=" C PHE F 156 " pdb=" N PRO F 157 " pdb=" CA PRO F 157 " ideal model delta harmonic sigma weight residual 180.00 -139.15 -40.85 0 5.00e+00 4.00e-02 6.68e+01 ... (remaining 9979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.894: 2476 3.894 - 7.787: 0 7.787 - 11.681: 0 11.681 - 15.574: 0 15.574 - 19.468: 2 Chirality restraints: 2478 Sorted by residual: chirality pdb=" S2 F3S A 602 " pdb="FE1 F3S A 602 " pdb="FE3 F3S A 602 " pdb="FE4 F3S A 602 " both_signs ideal model delta sigma weight residual False 10.77 -8.70 19.47 2.00e-01 2.50e+01 9.48e+03 chirality pdb=" S2 F3S D 602 " pdb="FE1 F3S D 602 " pdb="FE3 F3S D 602 " pdb="FE4 F3S D 602 " both_signs ideal model delta sigma weight residual False 10.77 -8.70 19.47 2.00e-01 2.50e+01 9.47e+03 chirality pdb=" CB ILE B 133 " pdb=" CA ILE B 133 " pdb=" CG1 ILE B 133 " pdb=" CG2 ILE B 133 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 2475 not shown) Planarity restraints: 2986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC C 502 " -0.019 2.00e-02 2.50e+03 4.68e-02 4.93e+01 pdb=" C2C HEC C 502 " 0.127 2.00e-02 2.50e+03 pdb=" C3C HEC C 502 " -0.006 2.00e-02 2.50e+03 pdb=" C4C HEC C 502 " -0.002 2.00e-02 2.50e+03 pdb=" CAC HEC C 502 " -0.034 2.00e-02 2.50e+03 pdb=" CHC HEC C 502 " -0.024 2.00e-02 2.50e+03 pdb=" CHD HEC C 502 " 0.004 2.00e-02 2.50e+03 pdb=" CMC HEC C 502 " -0.036 2.00e-02 2.50e+03 pdb=" NC HEC C 502 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC F 502 " -0.018 2.00e-02 2.50e+03 4.66e-02 4.89e+01 pdb=" C2C HEC F 502 " 0.127 2.00e-02 2.50e+03 pdb=" C3C HEC F 502 " -0.006 2.00e-02 2.50e+03 pdb=" C4C HEC F 502 " -0.003 2.00e-02 2.50e+03 pdb=" CAC HEC F 502 " -0.034 2.00e-02 2.50e+03 pdb=" CHC HEC F 502 " -0.024 2.00e-02 2.50e+03 pdb=" CHD HEC F 502 " 0.004 2.00e-02 2.50e+03 pdb=" CMC HEC F 502 " -0.036 2.00e-02 2.50e+03 pdb=" NC HEC F 502 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC F 503 " 0.013 2.00e-02 2.50e+03 2.95e-02 1.95e+01 pdb=" C2C HEC F 503 " -0.080 2.00e-02 2.50e+03 pdb=" C3C HEC F 503 " 0.005 2.00e-02 2.50e+03 pdb=" C4C HEC F 503 " -0.000 2.00e-02 2.50e+03 pdb=" CAC HEC F 503 " 0.022 2.00e-02 2.50e+03 pdb=" CHC HEC F 503 " 0.015 2.00e-02 2.50e+03 pdb=" CHD HEC F 503 " -0.002 2.00e-02 2.50e+03 pdb=" CMC HEC F 503 " 0.022 2.00e-02 2.50e+03 pdb=" NC HEC F 503 " 0.006 2.00e-02 2.50e+03 ... (remaining 2983 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 258 2.59 - 3.17: 15465 3.17 - 3.74: 25656 3.74 - 4.32: 37406 4.32 - 4.90: 59546 Nonbonded interactions: 138331 Sorted by model distance: nonbonded pdb=" SG CYS A 226 " pdb=" S1 F3S A 602 " model vdw 2.011 3.760 nonbonded pdb=" SG CYS D 226 " pdb=" S1 F3S D 602 " model vdw 2.012 3.760 nonbonded pdb=" SG CYS A 222 " pdb=" S3 F3S A 602 " model vdw 2.013 3.760 nonbonded pdb=" SG CYS D 222 " pdb=" S3 F3S D 602 " model vdw 2.013 3.760 nonbonded pdb=" OH TYR A 68 " pdb=" O PRO A 224 " model vdw 2.090 2.440 ... (remaining 138326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 5.700 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 49.930 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.030 1.774 16972 Z= 2.302 Angle : 1.485 52.370 23202 Z= 0.618 Chirality : 0.556 19.468 2478 Planarity : 0.006 0.078 2986 Dihedral : 15.658 132.892 6122 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.96 % Favored : 88.66 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.17), residues: 2072 helix: -1.63 (0.19), residues: 670 sheet: -1.40 (0.36), residues: 182 loop : -1.91 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP A 111 HIS 0.016 0.002 HIS D 503 PHE 0.034 0.004 PHE E 79 TYR 0.030 0.003 TYR D 368 ARG 0.011 0.001 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 86 PHE cc_start: 0.4663 (t80) cc_final: 0.4278 (t80) REVERT: B 148 LEU cc_start: 0.8433 (mt) cc_final: 0.8193 (mt) REVERT: B 150 TYR cc_start: 0.5574 (t80) cc_final: 0.5275 (t80) REVERT: C 410 GLU cc_start: 0.6098 (tp30) cc_final: 0.5835 (tp30) REVERT: E 86 PHE cc_start: 0.4701 (t80) cc_final: 0.4272 (t80) REVERT: E 148 LEU cc_start: 0.8457 (mt) cc_final: 0.8233 (mt) REVERT: E 150 TYR cc_start: 0.5648 (t80) cc_final: 0.5356 (t80) REVERT: F 135 TYR cc_start: 0.6874 (t80) cc_final: 0.6654 (t80) REVERT: F 410 GLU cc_start: 0.6060 (tp30) cc_final: 0.5821 (tp30) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2815 time to fit residues: 93.5021 Evaluate side-chains 180 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 10.0000 chunk 156 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 HIS ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 503 HIS ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.188 16972 Z= 0.279 Angle : 1.278 73.220 23202 Z= 0.491 Chirality : 0.048 0.582 2478 Planarity : 0.005 0.059 2986 Dihedral : 10.145 119.323 2432 Min Nonbonded Distance : 1.479 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.23 % Favored : 93.39 % Rotamer: Outliers : 0.82 % Allowed : 9.10 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.18), residues: 2072 helix: -0.47 (0.20), residues: 650 sheet: -0.68 (0.39), residues: 170 loop : -1.61 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 111 HIS 0.005 0.001 HIS D 503 PHE 0.016 0.001 PHE A 270 TYR 0.018 0.002 TYR C 120 ARG 0.005 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 201 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 150 TYR cc_start: 0.5378 (t80) cc_final: 0.4871 (t80) REVERT: C 182 HIS cc_start: 0.5775 (m-70) cc_final: 0.5228 (m170) REVERT: C 409 ASP cc_start: 0.5525 (t0) cc_final: 0.5300 (m-30) REVERT: E 86 PHE cc_start: 0.4226 (t80) cc_final: 0.4000 (t80) REVERT: E 150 TYR cc_start: 0.5425 (t80) cc_final: 0.4865 (t80) REVERT: F 182 HIS cc_start: 0.5647 (m-70) cc_final: 0.5174 (m170) REVERT: F 224 ASP cc_start: 0.7793 (p0) cc_final: 0.7441 (p0) outliers start: 14 outliers final: 8 residues processed: 207 average time/residue: 0.2633 time to fit residues: 84.7922 Evaluate side-chains 190 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 182 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 408 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 185 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 16972 Z= 0.317 Angle : 1.162 85.542 23202 Z= 0.457 Chirality : 0.065 1.625 2478 Planarity : 0.005 0.057 2986 Dihedral : 10.083 122.935 2432 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.92 % Favored : 91.80 % Rotamer: Outliers : 1.82 % Allowed : 13.50 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.19), residues: 2072 helix: -0.18 (0.21), residues: 656 sheet: -0.43 (0.40), residues: 166 loop : -1.57 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 111 HIS 0.006 0.001 HIS E 118 PHE 0.018 0.002 PHE D 270 TYR 0.017 0.002 TYR A 79 ARG 0.005 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 207 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7442 (tt) REVERT: C 118 MET cc_start: 0.7908 (tpt) cc_final: 0.7546 (tpt) REVERT: D 257 MET cc_start: 0.6302 (mtm) cc_final: 0.6075 (mtp) REVERT: E 86 PHE cc_start: 0.4480 (t80) cc_final: 0.4076 (t80) REVERT: F 118 MET cc_start: 0.7944 (tpt) cc_final: 0.7606 (tpt) REVERT: F 182 HIS cc_start: 0.5588 (m-70) cc_final: 0.5153 (m170) REVERT: F 224 ASP cc_start: 0.7785 (p0) cc_final: 0.7439 (p0) outliers start: 31 outliers final: 23 residues processed: 221 average time/residue: 0.2728 time to fit residues: 92.2361 Evaluate side-chains 215 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 191 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 408 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 53 optimal weight: 0.0970 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 ASN ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 16972 Z= 0.233 Angle : 1.095 83.816 23202 Z= 0.424 Chirality : 0.059 1.404 2478 Planarity : 0.005 0.058 2986 Dihedral : 9.785 118.100 2432 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.50 % Favored : 94.31 % Rotamer: Outliers : 2.99 % Allowed : 14.50 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.19), residues: 2072 helix: 0.16 (0.21), residues: 666 sheet: -0.16 (0.40), residues: 166 loop : -1.42 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 111 HIS 0.004 0.001 HIS C 308 PHE 0.017 0.001 PHE D 270 TYR 0.015 0.001 TYR D 443 ARG 0.005 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 209 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 VAL cc_start: 0.6633 (m) cc_final: 0.6430 (m) REVERT: C 118 MET cc_start: 0.8088 (tpt) cc_final: 0.7655 (tpt) REVERT: D 440 VAL cc_start: 0.6662 (m) cc_final: 0.6443 (m) REVERT: F 118 MET cc_start: 0.8077 (tpt) cc_final: 0.7517 (tpt) outliers start: 51 outliers final: 31 residues processed: 243 average time/residue: 0.2822 time to fit residues: 105.1550 Evaluate side-chains 228 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 197 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 408 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 ASN ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 16972 Z= 0.489 Angle : 1.249 84.992 23202 Z= 0.500 Chirality : 0.065 1.456 2478 Planarity : 0.006 0.062 2986 Dihedral : 10.461 130.778 2432 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.46 % Favored : 90.15 % Rotamer: Outliers : 3.76 % Allowed : 16.37 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.19), residues: 2072 helix: -0.24 (0.21), residues: 668 sheet: -0.47 (0.38), residues: 182 loop : -1.71 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 73 HIS 0.009 0.001 HIS B 118 PHE 0.022 0.003 PHE D 270 TYR 0.024 0.002 TYR E 150 ARG 0.004 0.001 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 204 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7465 (tt) REVERT: A 271 TYR cc_start: 0.7684 (m-80) cc_final: 0.7483 (m-80) REVERT: B 86 PHE cc_start: 0.4510 (t80) cc_final: 0.4062 (t80) REVERT: D 13 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7453 (tt) REVERT: E 86 PHE cc_start: 0.4509 (t80) cc_final: 0.4052 (t80) REVERT: F 224 ASP cc_start: 0.7754 (p0) cc_final: 0.7505 (p0) outliers start: 64 outliers final: 46 residues processed: 242 average time/residue: 0.2677 time to fit residues: 100.6491 Evaluate side-chains 247 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 199 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 408 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 0.8980 chunk 179 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 199 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 16972 Z= 0.228 Angle : 1.104 83.517 23202 Z= 0.426 Chirality : 0.059 1.437 2478 Planarity : 0.005 0.060 2986 Dihedral : 9.817 120.307 2432 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.69 % Favored : 94.11 % Rotamer: Outliers : 2.70 % Allowed : 18.13 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.19), residues: 2072 helix: 0.16 (0.21), residues: 666 sheet: 0.14 (0.41), residues: 168 loop : -1.44 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 111 HIS 0.004 0.001 HIS E 118 PHE 0.015 0.001 PHE D 270 TYR 0.020 0.001 TYR D 271 ARG 0.003 0.000 ARG F 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 214 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.6796 (t0) cc_final: 0.6594 (t0) REVERT: A 221 ASN cc_start: 0.8565 (t0) cc_final: 0.8156 (t0) REVERT: C 118 MET cc_start: 0.8196 (tpt) cc_final: 0.7924 (tpt) REVERT: D 57 ASP cc_start: 0.6897 (t0) cc_final: 0.6687 (t0) REVERT: D 221 ASN cc_start: 0.8541 (t0) cc_final: 0.8135 (t0) REVERT: D 226 CYS cc_start: 0.8481 (OUTLIER) cc_final: 0.6949 (p) REVERT: F 118 MET cc_start: 0.8205 (tpt) cc_final: 0.7933 (tpt) outliers start: 46 outliers final: 37 residues processed: 242 average time/residue: 0.2724 time to fit residues: 104.0208 Evaluate side-chains 239 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 201 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 368 TYR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 253 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 0.0070 chunk 22 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 167 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 198 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 121 optimal weight: 0.0870 chunk 91 optimal weight: 3.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 HIS ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 16972 Z= 0.212 Angle : 1.074 83.276 23202 Z= 0.413 Chirality : 0.059 1.439 2478 Planarity : 0.005 0.054 2986 Dihedral : 9.486 112.737 2432 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.12 % Favored : 94.74 % Rotamer: Outliers : 2.64 % Allowed : 18.60 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.19), residues: 2072 helix: 0.49 (0.21), residues: 664 sheet: -0.21 (0.41), residues: 168 loop : -1.18 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 111 HIS 0.004 0.001 HIS A 278 PHE 0.012 0.001 PHE A 270 TYR 0.019 0.001 TYR D 271 ARG 0.006 0.000 ARG F 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 212 time to evaluate : 1.803 Fit side-chains revert: symmetry clash REVERT: A 57 ASP cc_start: 0.6916 (t0) cc_final: 0.6688 (t0) REVERT: A 221 ASN cc_start: 0.8495 (t0) cc_final: 0.8240 (t0) REVERT: C 88 THR cc_start: 0.6777 (p) cc_final: 0.6565 (t) REVERT: D 57 ASP cc_start: 0.6951 (t0) cc_final: 0.6734 (t0) REVERT: F 456 MET cc_start: 0.5670 (tpt) cc_final: 0.4822 (tpp) outliers start: 45 outliers final: 38 residues processed: 240 average time/residue: 0.2723 time to fit residues: 99.6766 Evaluate side-chains 230 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 192 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 408 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 0.0070 chunk 79 optimal weight: 0.0570 chunk 118 optimal weight: 0.0980 chunk 59 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 156 optimal weight: 0.0070 overall best weight: 0.1334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN C 347 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 ASN ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 ASN F 347 HIS ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 16972 Z= 0.202 Angle : 1.069 83.233 23202 Z= 0.409 Chirality : 0.059 1.447 2478 Planarity : 0.005 0.054 2986 Dihedral : 9.315 106.226 2432 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.49 % Favored : 95.42 % Rotamer: Outliers : 2.11 % Allowed : 19.72 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.19), residues: 2072 helix: 0.67 (0.21), residues: 672 sheet: 0.06 (0.42), residues: 166 loop : -1.24 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 111 HIS 0.003 0.001 HIS A 278 PHE 0.009 0.001 PHE D 80 TYR 0.020 0.001 TYR C 135 ARG 0.006 0.000 ARG F 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 213 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.6986 (t0) cc_final: 0.6674 (t0) REVERT: A 211 ASP cc_start: 0.8110 (t70) cc_final: 0.6728 (t0) REVERT: A 221 ASN cc_start: 0.8408 (t0) cc_final: 0.8193 (t0) REVERT: B 160 PRO cc_start: 0.5711 (Cg_exo) cc_final: 0.5454 (Cg_endo) REVERT: C 182 HIS cc_start: 0.5615 (m-70) cc_final: 0.5053 (m170) REVERT: D 57 ASP cc_start: 0.6999 (t0) cc_final: 0.6704 (t0) REVERT: D 96 TYR cc_start: 0.8650 (t80) cc_final: 0.8214 (t80) REVERT: D 211 ASP cc_start: 0.8080 (t70) cc_final: 0.6692 (t0) REVERT: D 221 ASN cc_start: 0.8390 (t0) cc_final: 0.8181 (t0) REVERT: D 456 MET cc_start: 0.7022 (mmm) cc_final: 0.6241 (mtt) REVERT: E 160 PRO cc_start: 0.5761 (Cg_exo) cc_final: 0.5514 (Cg_endo) REVERT: F 182 HIS cc_start: 0.5596 (m-70) cc_final: 0.5043 (m170) REVERT: F 456 MET cc_start: 0.5465 (tpt) cc_final: 0.4540 (tpp) outliers start: 36 outliers final: 28 residues processed: 235 average time/residue: 0.2615 time to fit residues: 95.3627 Evaluate side-chains 225 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 197 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 129 TYR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 253 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 0.9980 chunk 190 optimal weight: 7.9990 chunk 173 optimal weight: 8.9990 chunk 185 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 167 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 184 optimal weight: 0.0980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 HIS ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 16972 Z= 0.241 Angle : 1.089 83.431 23202 Z= 0.418 Chirality : 0.059 1.451 2478 Planarity : 0.005 0.053 2986 Dihedral : 9.340 108.310 2432 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 2.00 % Allowed : 20.31 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.19), residues: 2072 helix: 0.65 (0.21), residues: 678 sheet: 0.04 (0.44), residues: 146 loop : -1.19 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 73 HIS 0.004 0.001 HIS A 278 PHE 0.011 0.001 PHE A 80 TYR 0.023 0.002 TYR C 135 ARG 0.008 0.000 ARG D 397 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 208 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.7010 (t0) cc_final: 0.6706 (t0) REVERT: A 211 ASP cc_start: 0.8157 (t70) cc_final: 0.6859 (t0) REVERT: A 221 ASN cc_start: 0.8481 (t0) cc_final: 0.8115 (t0) REVERT: A 456 MET cc_start: 0.6971 (mmm) cc_final: 0.6275 (mtt) REVERT: A 526 MET cc_start: 0.5513 (mtt) cc_final: 0.4819 (mtt) REVERT: B 160 PRO cc_start: 0.5956 (Cg_exo) cc_final: 0.5728 (Cg_endo) REVERT: D 57 ASP cc_start: 0.7001 (t0) cc_final: 0.6690 (t0) REVERT: D 211 ASP cc_start: 0.8125 (t70) cc_final: 0.6826 (t0) REVERT: D 221 ASN cc_start: 0.8505 (t0) cc_final: 0.8127 (t0) REVERT: D 456 MET cc_start: 0.6910 (mmm) cc_final: 0.6205 (mtt) REVERT: D 526 MET cc_start: 0.5609 (mtt) cc_final: 0.4931 (mtt) REVERT: E 160 PRO cc_start: 0.5974 (Cg_exo) cc_final: 0.5747 (Cg_endo) REVERT: F 182 HIS cc_start: 0.5613 (m-70) cc_final: 0.5043 (m170) REVERT: F 456 MET cc_start: 0.5593 (tpt) cc_final: 0.4672 (tpp) outliers start: 34 outliers final: 30 residues processed: 226 average time/residue: 0.2697 time to fit residues: 94.3605 Evaluate side-chains 230 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 200 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 408 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 4.9990 chunk 195 optimal weight: 0.8980 chunk 119 optimal weight: 0.0270 chunk 92 optimal weight: 2.9990 chunk 136 optimal weight: 0.0170 chunk 205 optimal weight: 9.9990 chunk 188 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 overall best weight: 0.5876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 HIS ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 16972 Z= 0.205 Angle : 1.069 83.255 23202 Z= 0.410 Chirality : 0.059 1.446 2478 Planarity : 0.004 0.048 2986 Dihedral : 9.294 106.644 2432 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.49 % Favored : 95.42 % Rotamer: Outliers : 1.76 % Allowed : 20.60 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.19), residues: 2072 helix: 0.88 (0.21), residues: 666 sheet: 0.15 (0.43), residues: 166 loop : -1.18 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 111 HIS 0.003 0.000 HIS A 278 PHE 0.009 0.001 PHE A 80 TYR 0.029 0.001 TYR C 135 ARG 0.008 0.000 ARG D 397 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 206 time to evaluate : 1.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.7061 (t0) cc_final: 0.6751 (t0) REVERT: A 96 TYR cc_start: 0.8686 (t80) cc_final: 0.8231 (t80) REVERT: A 221 ASN cc_start: 0.8423 (t0) cc_final: 0.8094 (t0) REVERT: A 456 MET cc_start: 0.6896 (mmm) cc_final: 0.6207 (mtt) REVERT: C 115 TYR cc_start: 0.7592 (m-80) cc_final: 0.7377 (m-80) REVERT: C 158 PHE cc_start: 0.5793 (m-80) cc_final: 0.5031 (m-80) REVERT: C 449 LYS cc_start: 0.6543 (pptt) cc_final: 0.5563 (ptpp) REVERT: D 57 ASP cc_start: 0.7021 (t0) cc_final: 0.6722 (t0) REVERT: D 96 TYR cc_start: 0.8679 (t80) cc_final: 0.8241 (t80) REVERT: D 221 ASN cc_start: 0.8413 (t0) cc_final: 0.8098 (t0) REVERT: D 456 MET cc_start: 0.6813 (mmm) cc_final: 0.6147 (mtt) REVERT: E 160 PRO cc_start: 0.5826 (Cg_exo) cc_final: 0.5624 (Cg_endo) REVERT: F 115 TYR cc_start: 0.7699 (m-80) cc_final: 0.7390 (m-80) REVERT: F 182 HIS cc_start: 0.5500 (m-70) cc_final: 0.4928 (m170) REVERT: F 456 MET cc_start: 0.5531 (tpt) cc_final: 0.4661 (tpp) outliers start: 30 outliers final: 30 residues processed: 220 average time/residue: 0.2523 time to fit residues: 87.4262 Evaluate side-chains 233 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 203 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 408 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 150 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 163 optimal weight: 0.0170 chunk 68 optimal weight: 0.1980 chunk 168 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 overall best weight: 0.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 HIS ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 HIS ** F 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.158459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.145479 restraints weight = 22506.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.144519 restraints weight = 29620.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.144902 restraints weight = 28723.681| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 16972 Z= 0.212 Angle : 1.072 83.332 23202 Z= 0.410 Chirality : 0.059 1.449 2478 Planarity : 0.004 0.048 2986 Dihedral : 9.216 105.777 2432 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.50 % Favored : 94.40 % Rotamer: Outliers : 2.23 % Allowed : 20.07 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.19), residues: 2072 helix: 0.93 (0.21), residues: 666 sheet: 0.00 (0.41), residues: 162 loop : -1.11 (0.19), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 111 HIS 0.003 0.000 HIS A 278 PHE 0.010 0.001 PHE D 270 TYR 0.027 0.001 TYR C 135 ARG 0.008 0.000 ARG D 397 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2954.83 seconds wall clock time: 55 minutes 44.08 seconds (3344.08 seconds total)